A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757693



Internal ID9633152
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:33385555..34041334hg38UCSC Ensembl
Innerchr19:33876461..34532239hg19UCSC Ensembl
Innerchr19:38568301..39224079hg18UCSC Ensembl
Innerchr19:38568301..39224079hg17UCSC Ensembl
Cytoband19q13.11
Allele length
AssemblyAllele length
hg38655780
hg19655779
hg18655779
hg17655779
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758755
Supporting Variantsessv14034, essv11295, essv22276
SamplesNA18862, NA12762, NA18863
Known GenesCHST8, KCTD15, PEPD
MethodSNP array
AnalysisThe algorithm used to call CNVs using the 500K EA platform was developed to accurately define CNV regions using a large set of reference samples and is described in detail in a separate publication (Komura 2006). The algorithm contains three major parts: 1) Intensity pre-processing using an improved version of Genomic Imbalance Map (GIM) (Ishikawa et al. 2005), including probe selection, noise reduction, normalization, and intensity ratio adjustment based on affinity differences between alleles of a SNP, 2) CNV extraction, which identifies CNVs from all pair-wise comparisons using a modified SW-ARRAY, and 3) A copy number inference step which utilizes signal ratios and SNP information to more precisely define CNV boundaries and the copy number within each region.
PlatformAffymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2757693
Frequency
Sample Size270
Observed Gain3
Observed Loss0
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer